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nanomaterials.yml
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nanomaterials.yml
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nanomaterial:
title: Nanomaterial Type
sub:
metals:
title: Metals
min_wulff_radius: 3
sub:
alm: Aluminum (Al)
acm: Actinium (Ac)
cam: Calcium (Ca)
cem: Cerium (Ce)
cum: Copper (Cu)
esm: Einsteinium (Es)
aum: Gold (Au)
aum_nanocluster:
name: Gold Nanocluster with Ligand (Au<sub>x</sub>SR<sub>y</sub>)
shapes: ""
ligand: true
pbc: "---"
core:
core_type:
type: select
label: Core Type
variable_title: core_type
default: au25
onchange: "update_system_volume()"
options:
au25: Au25(SR)18 (0.9 nm)
au36: Au36(SR)24 (1.1 nm)
au44: Au44(SR)28 (1.1 nm)
au68: Au68(SR)34 (1.2 nm)
au102: Au102(SR)44 (1.5 nm)
au133: Au133(SR)52 (1.7 nm)
au144: Au144(SR)60 (1.7 nm)
au246: Au246(SR)80 (2.2 nm)
au279: Au279(SR)84 (2.2 nm)
au314: Au314(SR)96 (2.3 nm)
ligand_morphology:
ligand_pattern:
type: select
label: Ligand Distribution
variable_title: ligand_pattern
default: random
allowed_nligands: ">1"
onchange: "check_allowed_vis()"
options:
random: Random
strip: Strip
janus: Janus
ligand_ratio_1:
type: text
label: "Ratio of ligand 1"
variable_title: ligand_ratio_1
default: 1
size: 3
allowed_nligands: ">1"
allowed_patterns: random
validation:
min: 1
ligand_ratio_2:
type: text
label: "Ratio of ligand 2"
variable_title: ligand_ratio_2
default: 1
size: 3
allowed_nligands: ">1"
allowed_patterns: random
validation:
min: 1
strip:
type: text
label: Number of Strips
variable_title: strip
default: 2
size: 3
allowed_nligands: ">1"
allowed_patterns: strip
validation:
min: 0
aum_nanoparticle:
name: Gold Nanoparticle with Ligand (Au<sub>x</sub>SR<sub>y</sub>)
shapes: ""
ligand: true
pbc: "---"
core:
core_type:
type: select
label: Core Type
variable_title: core_type
default: icosahedron
onchange: "check_allowed_vis()"
options:
icosahedron: Icosahedron
cube: Cube
attachment_pattern:
type: select
label: Attachment Type
variable_title: attachment_pattern
default: staple
allowed_cores: icosahedron
options:
"staple": Staple
"staple+bridge": "Staple & Bridge"
core_chirality:
type: select
label: Chirality
variable_title: core_chirality
allowed_cores: icosahedron
default: R
options:
R: R
S: S
core_x:
type: text
label: "X length (Å)"
variable_title: core_x
allowed_cores: cube
size: 5
default: "22"
onchange: "update_system_volume()"
validation:
min: 5
core_y:
type: text
label: "Y length (Å)"
variable_title: core_y
allowed_cores: cube
size: 5
default: "22"
onchange: "update_system_volume()"
validation:
min: 5
core_z:
type: text
label: "Z length (Å)"
variable_title: core_z
allowed_cores: cube
size: 5
default: "22"
onchange: "update_system_volume()"
validation:
min: 5
core_radius:
type: text
label: "Radius (Å)"
variable_title: core_radius
allowed_cores: icosahedron
size: 5
default: "22"
onchange: "update_system_volume()"
validation:
min: 5
ligand_morphology:
ligand_pattern:
type: select
label: Ligand Distribution
variable_title: ligand_pattern
default: random
allowed_nligands: ">1"
onchange: "check_allowed_vis()"
options:
random: Random
janus: Janus
ligand_ratio_1:
type: text
label: "Ratio of ligand 1"
variable_title: ligand_ratio_1
default: 1
size: 3
allowed_nligands: ">1"
allowed_patterns: random
validation:
min: 1
ligand_ratio_2:
type: text
label: "Ratio of ligand 2"
variable_title: ligand_ratio_2
default: 1
size: 3
allowed_nligands: ">1"
allowed_patterns: random
validation:
min: 1
strip:
type: text
label: Number of Strips
variable_title: strip
default: 2
size: 3
allowed_nligands: ">1"
allowed_patterns: strip
validation:
min: 0
coverage:
type: text
label: Coverage (%)
variable_title: ligand_coverage
default: 100
size: 3
validation:
min: 0
max: 100
aum_surface:
name: Gold Surface with Ligand (Au<sub>x</sub>SR<sub>y</sub>)
shapes: "box"
mindex: "001 111"
pbc: "++-"
ligand: true
ligand_morphology:
ligand_pattern:
type: select
label: Ligand Distribution
variable_title: ligand_pattern
default: random
allowed_nligands: ">1"
onchange: "check_allowed_vis()"
options:
random: Random
strip: Strip
ligand_ratio_1:
type: text
label: "Ratio of ligand 1"
variable_title: ligand_ratio_1
default: 1
size: 3
allowed_nligands: ">1"
allowed_patterns: random
validation:
min: 1
ligand_ratio_2:
type: text
label: "Ratio of ligand 2"
variable_title: ligand_ratio_2
default: 1
size: 3
allowed_nligands: ">1"
allowed_patterns: random
validation:
min: 1
strip_x:
type: text
label: "# Strips along X"
variable_title: strip_x
default: 2
size: 3
allowed_nligands: ">1"
allowed_patterns: strip
validation:
min: 0
strip_y:
type: text
label: "# Strips along Y"
variable_title: strip_y
default: 2
size: 3
allowed_nligands: ">1"
allowed_patterns: strip
validation:
min: 0
coverage:
type: text
label: Coverage (%)
variable_title: ligand_coverage
default: 100
size: 3
validation:
min: 0
max: 100
irm: Iridium (Ir)
fem: Iron (Fe)
pbm: Lead (Pb)
nim: Nickel (Ni)
pdm: Palladium (Pd)
ptm: Platinum (Pt)
rhm: Rhodium (Rh)
agm: Silver (Ag)
srm: Strontium (Sr)
thm: Thorium (Th)
ybm: Ytterbium (Yb)
metaloxide:
title: Metal Oxides
sub:
ao:
name: "Aluminum Oxide (Al<sub>2</sub>O<sub>3</sub>)"
shapes: box
mindex: "001"
fo:
name: "Iron Oxide (Fe<sub>2</sub>O<sub>3</sub>)"
shapes: box
mindex: "001"
cro:
name: "Chromium Oxide (Cr<sub>2</sub>O<sub>3</sub>)"
shapes: box
mindex: "001"
cao:
name: "Calcium Oxide (CaO)"
shapes: box
mindex: "001"
mgo:
name: "Magnesium Oxide (MgO)"
shapes: box
mindex: "001"
nio:
name: "Nickel Oxide (NiO)"
shapes: box
mindex: "001"
metalhydroxide:
title: Metal Hydroxides
sub:
cah:
name: "Calcium Hydroxide (CaOH<sub>2</sub>)"
shapes: box
mindex: "001"
nih:
name: "Nickel Hydroxide (NiOH<sub>2</sub>)"
shapes: box
mindex: "001"
clay_minerals:
title: Clay Minerals
sub:
kn:
name: "Kaolinite (Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(OH)<sub>4</sub>)"
shapes: box
mindex: "001"
pp:
name: "Pyrophyllite (Al<sub>2</sub>Si<sub>4</sub>O<sub>10</sub>(OH)<sub>2</sub>)"
shapes: box
mindex: "001"
mm:
name: "Montmorillonite ((K, Na)<sub>n</sub>[Si<sub>4</sub>O<sub>8</sub>][Al<sub>2-n</sub>Mg<sub>n</sub>O<sub>2</sub>(OH)<sub>2</sub>])"
shapes: box
mindex: "001"
ion:
defect_ratio:
label: "(K, Na)<sub>x</sub>[Si<sub>4</sub>O<sub>8</sub>][Al<sub>(2-x)</sub>Mg<sub>x</sub>O<sub>2</sub>(OH<sub>2</sub>)]<br />(0 ≤ x < 0.95)"
default: 0
size: 7
variable_title: Ion Ratio
validation:
max: 0.95
min: 0
ion_type:
type: select
label: Ion Type
default: POT
options:
POT: "Potassium (Kᐩ)"
SOD: "Sodium (Naᐩ)"
info_table:
title: Ratio of Defect Recommendations
pH_info:
label: "CEC (mmol / 100 g)"
cells: [87, 90, 108, 143]
ionization_info:
label: x
cells: [0.321, 0.333, 0.400, 0.533]
mica:
title: Mica
sub:
mc:
name: "Muscovite (KAl<sub>2</sub>(AlSi<sub>3</sub>)O<sub>10</sub>(OH)<sub>2</sub>)"
shapes: box
mindex: "001"
calcium_sulfates:
title: Calcium Sulfates
sub:
gs:
name: Gypsum (CaSO<sub>4</sub>·2H<sub>2</sub>O)
mindex: "001 010 011 120 -111"
shapes: box wulff
min_mindices: 3
max_mindices: 3
min_wulff_radius: 14
hh:
name: Hemihydrate (2CaSO<sub>4</sub>·H<sub>2</sub>O)
mindex: "001 100"
shapes: box
ah:
name: Anhydrite (CaSO<sub>4</sub>)
mindex: "001"
shapes: box
cement_minerals:
title: Cement Minerals
sub:
ta:
name: "Tricalcium Aluminate (Ca<sub>3</sub>Al<sub>2</sub>O<sub>6</sub>)"
mindex: "010"
shapes: box
surf:
qhyd:
type: select
label: Hydration
default: dry
variable_title: Surface Hydration
options:
dry: Dry
wet: Wet
onchange: "handle_hydration(this)"
ts:
name: "Tricalcium Silicate (Ca<sub>3</sub>SiO<sub>5</sub>)"
mindex: "001 010 100"
min_mindices: 3
min_wulff_radius: 7
shapes: box wulff
surf:
qhyd:
type: select
label: Hydration
default: dry
variable_title: Surface Hydration
options:
dry: Dry
wet: Wet
onchange: "handle_hydration(this)"
#ettr: Ettringite
calcium_silicates:
title: Calcium Silicate Hydrates
sub:
tb:
name: Tobermorite (Ca<sub>4</sub>Si<sub>6</sub>O<sub>15</sub>(OH)<sub>2</sub>·5H<sub>2</sub>O)
mindex: "004"
shapes: box
silicate_minerals:
title: Silica
sub:
cr:
name: "α-Cristobalite (SiO<sub>2</sub>)"
shapes: box sphere
mindex: "20-2"
min_radius: 9
surf:
ion_percent:
label: "Degree of Ionization (%)<br />(Si-OH > Si-O<sup>-</sup>Na<sup>+</sup>; max: 50%)"
default: 0
size: 7
variable_title: Degree of Ionization
allowed_periods: " x y z xy yz xz"
validation:
max: 50
min: 0
surf_conc:
label: "Surface Concentration of Si-OH<br />(only xy periodicity, 0 ≤ c ≤ 9.0 unit/nm<sup>2</sup>)"
default: "4.7"
size: 7
allowed_periods: xy
allowed_shapes: box
variable_title: Surface Density
validation:
max: 9.0
min: 0
info_table:
title: Ionization Recommendations
pH_info:
label: pH
cells: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
ionization_info:
label: Ionization Degree (%)
cells: [0, 3.3, 6.6, 10.0, 13.3, 16.6, 20.0, 23.3, 26.6, 30.0]
qz:
name: "α-Quartz (SiO<sub>2</sub>)"
shapes: box sphere
mindex: "001"
min_radius: 5
surf:
ion_percent:
label: "Degree of Ionization (%)<br />(Si-OH > Si-O<sup>-</sup>Na<sup>+</sup>, default: 0, max: 50)"
default: 0
size: 7
allowed_periods: " x y z xy yz xz"
validation:
max: 50
min: 0
info_table:
title: Ionization Recommendations
pH_info:
label: pH
cells: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
ionization_info:
label: Ionization Degree (%)
cells: [0, 3.3, 6.6, 10.0, 13.3, 16.6, 20.0, 23.3, 26.6, 30.0]
other_minerals:
title: Phosphate minerals
sub:
ha:
name: "Hydroxyapatite (Ca<sub>5</sub>(PO<sub>4</sub>)<sub>3</sub>(OH))"
shapes: box wulff
min_wulff_radius: 5
mindex: "001 010 020 101"
pbc: "++-"
surf:
pH:
type: select
label: Environment pH
default: ha_basic
variable_title: Environment pH
onchange: "handle_pH(this)"
options:
ha_stbasic: "> 14"
ha_basic: "~ 10"
ha_acidic: "~ 5"
# aspect_ratio:
# label: Aspect Ratio
# default: 1
# variable_title: Aspect Ratio
# allowed_shapes: wulff
# size: 7
# validation:
# min: 0
transition_metal_chalcogenitides:
title: Transition Metal Dichalcogenides
sub:
md:
name: "Molybdenum Disulfide (MoS<sub>2</sub>)"
mindex: "001"
shapes: box
pbc: "++u"
info_table:
title: "Unit Cell Info"
unitcell_x:
label: Unit Cell X
cells: [""]
unitcell_y:
label: Unit Cell Y
cells: [""]
unitcell_z:
label: Unit Cell Z
cells: [""]
layer_dim:
label: Layer Dimension
cells: [""]
nlayers:
label: Number of Layers
cells: ["N/A"]
carbon_materials:
title: Carbonaceous Materials
sub:
tube:
name: Carbon Nanotube (CNT)
shapes: ""
pbc: 1
general:
chirality:
label: "Chirality (n, m)"
sep: ', '
fields:
chirality_n:
default: 3
variable_title: chirality_n
size: 3
onchange: "update_system_volume()"
chirality_m:
default: 3
variable_title: chirality_m
size: 3
onchange: "update_system_volume()"
cell_copies:
label: Cell Copies
type: text
default: 1
size: 3
onchange: "update_system_volume()"
filltube:
label: Fill tube with water
type: checkbox
variable_title: filltube
allowed_systype: solution
allowed_pbc: x y z
onchange: "update_system_volume()"
velectron:
variable_title: Virtual Electron
label: Use virtual electron model
type: checkbox
checked: false
info_table:
title: Calculated Tube Info
onload: "update_system_volume()"
tube_length:
type: span
label: Tube Length
suffix: " Å"
tube_diameter:
type: span
label: Tube Diameter
suffix: " Å"
tube_conductivity:
type: strong
label: Tube Conductivity
type: strong
tube_system_volume:
type: span
label: "System Volume"
suffix: " Å<sup>3</sup>"
gp:
name: Graphene
shapes: "box"
pbc: "uuu"
mindex: "001"
general:
n_rings:
variable_title: Number of Rings
label: Number of Rings
default: 100
size: 3
allowed_defect: ">0"
onchange: "update_grap_runtime_estimate(this)"
percent_defect:
variable_title: Percent Defect
label: Percent Defect
default: 0
size: 3
validation:
min: 0
onchange: "toggle_defect(this)"
velectron:
variable_title: Virtual Electron
label: Use virtual electron model
type: checkbox
checked: false
allowed_defect: "0"
dense_defect:
type: checkbox
variable_title: Dense defect
label: Dense Defect
checked: false
allowed_defect: ">0"
runtime_estimate:
type: span
label: Estimated Runtime
allowed_defect: ">0"
info_table:
title: "Unit Cell Info"
unitcell_x:
label: Unit Cell X
cells: [""]
unitcell_y:
label: Unit Cell Y
cells: [""]
unitcell_z:
label: Unit Cell Z
cells: [""]
layer_dim:
label: Layer Dimension
cells: [""]
nlayers:
label: Number of Layers
cells: ["N/A"]
gi:
name: Graphite
shapes: "box"
pbc: "uuu"
mindex: "001"
general:
velectron:
variable_title: Virtual Electron
label: Use virtual electron model
type: checkbox
checked: false
info_table:
title: "Unit Cell Info"
unitcell_x:
label: Unit Cell X
cells: [""]
unitcell_y:
label: Unit Cell Y
cells: [""]
unitcell_z:
label: Unit Cell Z
cells: [""]
layer_dim:
label: Layer Dimension
cells: [""]
nlayers:
label: Number of Layers
cells: ["N/A"]